How columnar transposition works
The message is written in rows under a keyword, one letter per column. Then the columns are read top to bottom, in the alphabetical order of the keyword's letters. Nothing is swapped for another letter, the letters just change places, so the letter counts still look like normal English.
If a keyword has the same letter twice, the one further left is read first. CacheCrack shows the column order it used. Spaces are usually removed before encoding, so leave "Remove spaces first" on unless the puzzle kept them.
Example
EVLNACDTESEAROFODEECWIREE with the keyword ZEBRAS decodes to WEAREDISCOVEREDFLEEATONCE.